Trying to register cisco 7942G with Freepbx End Point Manager failed

The missing files are not a problem. The phone is getting the main file it needs which is the SEPxxx.cnf file.

The phone you’re using will also provision over HTTP on port 6970 - you may want to try that instead if you are having problems with TFTP.

Pay attention to @Stewart1 suggestion - you need to turn off the NAT handling for these phones.